Volume 20, Number 1—January 2014
Research
Progenitor “Mycobacterium canettii” Clone Responsible for Lymph Node Tuberculosis Epidemic, Djibouti
Table 2
Sequence analysis of CRISPRs alleles of the Mycobacterium canettii isolates, Djibouti, 2010–2013*
Cluster | Strain | No. spacers | Allele code† | Alias‡ (accession no.) |
---|---|---|---|---|
A | Percy3 and all other clone A strains | 26 | III-A-69@94 | STB-D CIPT140060008 (NC_019950) |
C | Percy1004 | 12 | III-A-69@74-95-96-89@91-94 | |
C | Percy32 | 30 | III-A-69@74-95@98-75@91-94 | |
C | CIPT140010059 | 29 | III-A-69@74-95@98-75@91-94 | STB-A CIPT140010059 (NC_015848) |
– | Percy79 | 31 | III-A-99@129 | |
– | Percy301 | 31 | III-A-99@129 | |
B | Percy214 | 8 | I-C-130@137 | STB-H CIPT140070013 |
B | Percy525 | 8 | I-C-130@137 | |
C | Percy1101 | 14 | I-C-130@143 | |
– | Percy25 | 7 | I-C-131-132-144@148 | STB-E CIPT140070002 |
– | Percy65 | 27 (1 doublet) | I-C-201@205-203-206@226 | STB-J CIPT140070017 (NC_019952) |
– | Percy327 | 9 | I-C-130-133@137-198@200 | STB-L CIPT140070008 (NC_019965) |
– | Percy302 | 50; 53 | I-C-149@191-178var-192@197;I-Cvar-337@389 | STB-K CIPT140070010 (NC_019951) |
– | Percy89 | 83 | I-E-228-230@232-88var-233@240-245@258-278@333 | STB-G CIPT140070005 |
– | Percy99b | 58 | I-E-227@232-88var-233 @280-334@336 | STB-I CIPT140070007 |
– | Percy157 | 52 | I-E-227@232-88var-233@277 |
*CRISPR, clustered regularly interspaced short palindromic repeats.
†The CRISPR type is indicated as prefix (type III-A, I-C, I-Cvar, I-E). Allele codes refer to the spacers dictionary (Technical Appendix 2 Table 1). "69@94" indicates that all spacers from 69 to 94 are present. Spacers 1 to 68 have been previously reported in M. tuberculosis (9). Spacer numbering in "M. canettii" runs from 69 up to 389, i.e., the total number of spacers observed in M. canettii is 321.
‡Strains sequenced by (5) as draft or completed (European Nucleotide Archive accession no. indicated) genome 88var = TCCAGAGGTCGAAGTGATGTTCGGTGTTCTCCT.